Add PredictTcellActivation

Author: bbimber

singlecell/resources/chunks/AppendMetadata.R

@@ -4,9 +4,16 @@ if (!file.exists(netRc)) {
     stop(paste0('Unable to find file: ', netRc))
 }
 
-invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc, timeout = 60, timeout_ms = 60000))
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc, timeout = 60, timeout_ms = 60000, connecttimeout = 20, connecttimeout_ms = 20000))
 Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
 
+curlOpt <- curl::curl_options('timeout')
+logger::log_info('Curl options:')
+for (x in names(curlOpt)) {
+    logger::log_info(paste0(x, ': ', curlOpt[x]))
+}
+rm(curlOpt)
+
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])

singlecell/resources/chunks/PredictTcellActivation.R

@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+  printName(datasetId)
+  seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+  seuratObj <- PredictTcellActivation(seuratObj)
+
+  saveData(seuratObj, datasetId)
+
+  # Cleanup
+  rm(seuratObj)
+  gc()
+}

singlecell/resources/chunks/StudyMetadata.R

@@ -8,9 +8,9 @@ invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc, timeout = 60, timeo
 Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
 
 curlOpt <- curl::curl_options('timeout')
-message('Curl options:')
+logger::log_info('Curl options:')
 for (x in names(curlOpt)) {
-    message(paste0(x, ': ', curlOpt[x]))
+    logger::log_info(paste0(x, ': ', curlOpt[x]))
 }
 rm(curlOpt)
 

singlecell/src/org/labkey/singlecell/SingleCellModule.java

@@ -79,6 +79,7 @@
 import org.labkey.singlecell.pipeline.singlecell.PlotAssayFeatures;
 import org.labkey.singlecell.pipeline.singlecell.PlotAverageCiteSeqCounts;
 import org.labkey.singlecell.pipeline.singlecell.PredictScTour;
+import org.labkey.singlecell.pipeline.singlecell.PredictTcellActivation;
 import org.labkey.singlecell.pipeline.singlecell.PrepareRawCounts;
 import org.labkey.singlecell.pipeline.singlecell.RemoveCellCycle;
 import org.labkey.singlecell.pipeline.singlecell.RunCellHashing;
@@ -303,6 +304,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new RunTricycle.Provider());
         SequencePipelineService.get().registerPipelineStep(new ApplyKnownClonotypicData.Provider());
         SequencePipelineService.get().registerPipelineStep(new CalculateTcrRepertoireStats.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PredictTcellActivation.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

singlecell/src/org/labkey/singlecell/pipeline/singlecell/PredictTcellActivation.java

@@ -0,0 +1,37 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.List;
+
+public class PredictTcellActivation extends AbstractRDiscvrStep
+{
+    public PredictTcellActivation(PipelineContext ctx, PredictTcellActivation.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("PredictTcellActivation", "Predict T cell Activation", "RIRA", "This uses RIRA::PredictTcellActivation to predict TCR-triggered T cells", List.of(), null, null);
+        }
+
+
+        @Override
+        public PredictTcellActivation create(PipelineContext ctx)
+        {
+            return new PredictTcellActivation(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "tca";
+    }
+}
+